When creating molecular animations, especially those used to present molecular assemblies or docking processes, a common challenge arises: how to make sure certain atoms or molecular components stay fixed while others move? Let’s say you’re animating a ligand docking into a protein. You want the ligand to move, but the protein should remain stationary—at least partially. Without the ability to hold parts of the system in place, the animation might look confusing or inaccurate.
This is where SAMSON’s Hold atoms animation effect offers a direct solution.
What Does “Hold atoms” Do?
The Hold atoms animation in SAMSON allows modelers to fix the positions of selected atoms between two animation frames. This is particularly helpful in scenarios where you want to clearly illustrate the motion of only part of a molecular system, making your presentation more focused and easier to interpret.
Imagine you’re showing a drug molecule moving toward a binding site. You want viewers to focus on the movement of the ligand—not on unintended motions of the larger macromolecule. By using Hold atoms, you can freeze the protein in place and let the ligand be the star of the show.
How to Use “Hold atoms”
Here’s a step-by-step guide to using this feature in SAMSON:
- Select the atoms or groups of particles in your molecular system that you want to hold in place. You can do this by using the selection tools in SAMSON. For more details, see the selection guide.
- Navigate to the Animation panel of the Animator.
- Double-click on the Hold atoms animation effect.
- SAMSON will automatically link the holding of atom positions between the two keyframes. You can adjust these keyframes to align with other movements in your animation timeline.
You’re now set up to animate only the parts of your molecular system that matter for your current visualization. The result is not only more precise but also more engaging for viewers.
Example in Action
Below is a visual example of how Hold atoms works alongside a movement animation. In this animated gif, you can see one part of the molecular system remaining fixed while another part moves:
This clarity is especially valuable when preparing presentations for interdisciplinary teams or for educational use, where too much motion can make it difficult to distinguish between the components of the system.
Ready-Made Examples to Explore
SAMSON Connect offers several user-created documents that show how Hold atoms is used in practice:
These examples can provide inspiration or templates for your own animations.
To learn more about the Hold atoms animation feature, visit the full documentation page here: https://documentation.samson-connect.net/users/latest/animations/hold-atoms/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.